Plasminogen activator inhibitor-1 (PAI-1) is a biologically important serine protease inhibitor (serpin) that, when overexpressed, is associated with a high risk for cardiovascular disease and cancer metastasis. Several of its ligands, including vitronectin, tissue-type and urokinase-type plasminogen activator (tPA, uPA), affect the fate of PAI-1. Here, we measured changes in the solvent accessibility and dynamics of an important unresolved functional region, the reactive center loop (RCL), upon binding of these ligands. Binding of the catalytically inactive S195A variant of tPA to the RCL causes an increase in fluorescence, indicating greater solvent protection, at its C-terminus, while mobility along the loop remains relatively unchanged. In contrast, a fluorescence increase and large decrease in mobility at the N-terminal RCL is observed upon binding of S195A-uPA to PAI-1. At a site distant from the RCL, binding of vitronectin results in a modest decrease in fluorescence at its proximal end without restricting overall loop dynamics. These results provide the new evidence for ligand effects on RCL conformation and dynamics and differences in the Michaelis complex with plasminogen activators that can be used for the development of more specific inhibitors to PAI-1. This study is also the first to use electron paramagnetic resonance (EPR) spectroscopy to investigate PAI-1 dynamics. This article is protected by copyright. All rights reserved.

Fluorescent proteins (FPs) are powerful tools for cell and molecular biology. Here we report that based on structural analysis, we have rationally designed a blue-shifted mutant of a recently engineered monomeric infrared fluorescent protein (mIFP). This variant, named iBlueberry, bears a single mutation that shifts both excitation and emission spectra by ∼40 nm. Furthermore, iBlueberry is four times more photostable than mIFP, rendering it more advantageous for imaging protein dynamics. By tagging iBlueberry to centrin, we demonstrate that the fusion protein labels the centrosome in the developing zebrafish embryo. Together with GFP-labeled nucleus and tdTomato-labeled plasma membrane, we performed time-lapse imaging to visualize the dynamics of centrosomes in radial glia neural progenitors in the intact zebrafish brain. We further show that iBlueberry can be used together with mIFP in two-color protein labeling in living cells and in two-color tumor labeling in mice. This article is protected by copyright. All rights reserved.

Allosteric ligands for the pharmacologically dark receptors GPR68 and GPR65

Nature 527, 7579 (2015). doi:10.1038/nature15699

Authors: Xi-Ping Huang, Joel Karpiak, Wesley K. Kroeze, Hu Zhu, Xin Chen, Sheryl S. Moy, Kara A. Saddoris, Viktoriya D. Nikolova, Martilias S. Farrell, Sheng Wang, Thomas J. Mangano, Deepak A. Deshpande, Alice Jiang, Raymond B. Penn, Jian Jin, Beverly H. Koller, Terry Kenakin, Brian K. Shoichet & Bryan L. Roth

At least 120 non-olfactory G-protein-coupled receptors in the human genome are ‘orphans’ for which endogenous ligands are unknown, and many have no selective ligands, hindering the determination of their biological functions and clinical relevance. Among these is GPR68, a proton receptor that lacks small molecule

Extra adsorption and adsorbate superlattice formation in metal-organic frameworks

Nature 527, 7579 (2015). doi:10.1038/nature15734

Authors: Hae Sung Cho, Hexiang Deng, Keiichi Miyasaka, Zhiyue Dong, Minhyung Cho, Alexander V. Neimark, Jeung Ku Kang, Omar M. Yaghi & Osamu Terasaki

Metal-organic frameworks (MOFs) have a high internal surface area and widely tunable composition, which make them useful for applications involving adsorption, such as hydrogen, methane or carbon dioxide storage. The selectivity and uptake capacity of the adsorption process are determined by interactions involving the adsorbates and their porous host materials. But, although the interactions of adsorbate molecules with the internal MOF surface and also amongst themselves within individual pores have been extensively studied, adsorbate–adsorbate interactions across pore walls have not been explored. Here we show that local strain in the MOF, induced by pore filling, can give rise to collective and long-range adsorbate–adsorbate interactions and the formation of adsorbate superlattices that extend beyond an original MOF unit cell. Specifically, we use in situ small-angle X-ray scattering to track and map the distribution and ordering of adsorbate molecules in five members of the mesoporous MOF-74 series along entire adsorption–desorption isotherms. We find in all cases that the capillary condensation that fills the pores gives rise to the formation of ‘extra adsorption domains’—that is, domains spanning several neighbouring pores, which have a higher adsorbate density than non-domain pores. In the case of one MOF, IRMOF-74-V-hex, these domains form a superlattice structure that is difficult to reconcile with the prevailing view of pore-filling as a stochastic process. The visualization of the adsorption process provided by our data, with clear evidence for initial adsorbate aggregation in distinct domains and ordering before an even distribution is finally reached, should help to improve our understanding of this process and may thereby improve our ability to exploit it practically.

We define a variant of \(k\) -of- \(n\) testing that we call conservative \(k\) -of- \(n\) testing. We present a polynomial-time, combinatorial algorithm for the problem of maximizing throughput of conservative \(k\) -of- \(n\) testing, in a parallel setting. This extends previous work of Condon et al. and Kodialam who presented combinatorial algorithms for parallel pipelined filter ordering, which is the special case where \(k=1\) (or \(k=n\) ). We also give a polynomial-time algorithm for maximizing throughput for standard \(k\) -of- \(n\) testing, based on the ellipsoid method, using previous techniques.

The metalloprotease PrtV from Vibrio cholerae serves an important function for the ability of bacteria to invade the mammalian host cell. The protein belongs to the family of M6 proteases, with a characteristic zinc ion in the catalytic active site. PrtV constitutes a 918 amino acids (102 kDa) multidomain pre-pro-protein that undergoes several N- and C-terminal modifications to form a catalytically active protease. We report here the NMR structure of the PrtV N-terminal domain (residues 23–103) that contains two short α-helices in a coiled coil motif. The helices are held together by a cluster of hydrophobic residues. Approximately 30 residues at the C-terminal end, which were predicted to form a third helical structure, are disordered. These residues are highly conserved within the genus Vibrio, which suggests that they might be functionally important.

Resistance to sodium carbonate extraction is regarded as a canonical way to distinguish integral membrane proteins (MPs) from other membrane-associated proteins. However, it has been observed that carbonate extraction releases some mitochondrial integral MPs. Here, by analyzing both artificially designed and native mitochondrial inner MPs containing transmembrane domains (TMDs) of different hydrophobicities, we show that carbonate treatment can release moderately hydrophobic TMDs from the mitochondrial inner membrane. These results suggest that resistance and sensitivity to carbonate extraction may be interpreted with caution when analyzing the nature of mitochondrial inner MPs.

Antibodies (Abs) are a crucial component of the immune system and are often used as diagnostic and therapeutic agents. The need for high-affinity and high-specificity antibodies in research and medicine is driving the development of computational tools for accelerating antibody design and discovery. We report a diverse set of antibody binding data with accompanying structures that can be used to evaluate methods for modeling antibody interactions. Our Antibody-Bind (AB-Bind) database includes 1101 mutants with experimentally determined changes in binding free energies (ΔΔG) across 32 complexes. Using the AB-Bind data set, we evaluated the performance of protein scoring potentials in their ability to predict changes in binding free energies upon mutagenesis. Numerical correlations between computed and observed ΔΔG values were low (r = 0.16–0.45), but the potentials exhibited predictive power for classifying variants as improved vs weakened binders. Performance was evaluated using the area under the curve (AUC) for receiver operator characteristic (ROC) curves; the highest AUC values for 527 mutants with |ΔΔG| > 1.0 kcal/mol were 0.81, 0.87, and 0.88 using STATIUM, FoldX, and Discovery Studio scoring potentials, respectively. Some methods could also enrich for variants with improved binding affinity; FoldX and Discovery Studio were able to correctly rank 42% and 30%, respectively, of the 80 most improved binders (those with ΔΔG < −1.0 kcal/mol) in the top 5% of the database. This modest predictive performance has value but demonstrates the continuing need to develop and improve protein energy functions for affinity prediction.

The effect of a mutation on protein stability is traditionally measured by genetic construction, expression, purification and physical analysis using low-throughput methods. This process is tedious and limits the number of mutants able to be examined in a single study. In contrast, functional fitness effects can be measured in a high-throughput manner by various deep mutational scanning tools. Using protein GB 1, we have recently demonstrated the feasibility of estimating the mutational stability effect (ΔΔG) of single-substitution based on the functional fitness profile of all double-substitutions. The principle is to identify genetic backgrounds that have an exhausted stability margin. The functional effect of an additional substitution on these genetic backgrounds can then be used to compute the mutational ΔΔG based on the biophysical relationship between functional fitness and thermodynamic stability. However, to identify such genetic backgrounds, the approach described in our previous study required a benchmark dataset, which is a set of known mutational ΔΔG. In this study, a benchmark-independent approach is developed. The genetic backgrounds of interest are identified using k-means clustering with the integration of structural information. We further demonstrated that a reasonable approximation of ΔΔG can also be obtained without taking structural information into account. In summary, this study describes a novel method for computing ΔΔG from double-substitution functional fitness profiles alone, without relying on any known mutational ΔΔG as a benchmark. This article is protected by copyright. All rights reserved.

Obtaining a quantitative description of the membrane proteins stability is crucial for understanding many biological processes. However the advance in this direction has remained a major challenge for both experimental studies and molecular modeling. One of the possible directions is the use of coarse-grained models but such models must be carefully calibrated and validated. Here we use a recent progress in benchmark studies on the energetics of amino acid residue and peptide membrane insertion and membrane protein stability in refining our previously developed coarse-grained model (Vicatos et al Proteins 2014; 82: 1168). Our refined model parameters were fitted and/or tested to reproduce water/membrane partitioning energetics of amino acid side chains and a couple of model peptides. This new model provides a reasonable agreement with experiment for absolute folding free energies of several β-barrel membrane proteins as well as effects of point mutations on a relative stability for one of those proteins, OmpLA. The consideration and ranking of different rotameric states for a mutated residue was found to be essential to achieve satisfactory agreement with the reference data. This article is protected by copyright. All rights reserved.

The projection games (aka Label Cover) problem is of great importance to the field of approximation algorithms, since most of the NP-hardness of approximation results we know today are reductions from Label Cover. In this paper we design several approximation algorithms for projection games: (1) A polynomial-time approximation algorithm that improves on the previous best approximation by Charikar et al. (Algorithmica 61(1):190–206, 2011). (2) A sub-exponential time algorithm with much tighter approximation for the case of smooth projection games. (3) A polynomial-time approximation scheme (PTAS) for projection games on planar graphs and a tight running time lower bound for such approximation schemes. The conference version of this paper had only the PTAS but not the running time lower bound.

The AbgT family of transporters was thought to contribute to bacterial folate biosynthesis by importing the catabolite p-aminobenzoyl-glutamate for producing this essential vitamin. Approximately 13,000 putative transporters of the family have been identified. However, before our work, no structural information was available and even functional data were minimal for this family of membrane proteins. To elucidate the structure and function of the AbgT family of transporters, we recently determined the X-ray structures of the full-length Alcanivorax borkumensis YdaH and Neisseria gonorrhoeae MtrF membrane proteins. The structures reveal that these two transporters assemble as dimers with architectures distinct from all other families of transporters. Both YdaH and MtrF are bowl-shaped dimers with a solvent-filled basin extending from the cytoplasm halfway across the membrane bilayer. The protomers of YdaH and MtrF contain nine transmembrane helices and two hairpins. These structures directly suggest a plausible pathway for substrate transport. A combination of the crystal structure, genetic analysis and substrate accumulation assay indicates that both YdaH and MtrF behave as exporters, capable of removing the folate metabolite p-aminobenzoic acid from bacterial cells. Further experimental data based on drug susceptibility and radioactive transport assay suggest that both YdaH and MtrF participate as antibiotic efflux pumps, importantly mediating bacterial resistance to sulfonamide antimetabolite drugs. It is possible that many of these AbgT-family transporters act as exporters, thereby conferring bacterial resistance to sulfonamides. The AbgT-family transporters may be important targets for the rational design of novel antibiotics to combat bacterial infections.

Magnetotactic bacteria (MTB) are a group of Gram-negative microorganisms that are able to sense and change their orientation in accordance with the geomagnetic field. This unique capability is due to the presence of a special suborganelle called the magnetosome, composed of either a magnetite or gregite crystal surrounded by a lipid membrane. MTB were first detected in 1975 and since then numerous efforts have been made to clarify the special mechanism of magnetosome formation at the molecular level. Magnetosome formation can be divided into several steps, beginning with vesicle invagination from the cell membrane, through protein sorting, followed by the combined steps of iron transportation, biomineralization, and the alignment of magnetosomes into a chain. The magnetosome-chain enables the sensing of the magnetic field, and thus, allows the MTB to navigate. It is known that magnetosome formation is tightly controlled by a distinctive set of magnetosome-associated proteins that are encoded mainly in a genomically conserved region within MTB called the magnetosome island (MAI). Most of these proteins were shown to have an impact on the magnetism of MTB. Here, we describe the process in which the magnetosome is formed with an emphasis on the different proteins that participate in each stage of the magnetosome formation scheme.

The week in science: 23–29 October 2015

Nature 526, 7575 (2015). http://www.nature.com/doifinder/10.1038/526614a

Martian landing-site selected; telescope shuttered in Hawaii; and Hurricane Patricia pounds Mexico.

Microbiology: Create a global microbiome effort

Nature 526, 7575 (2015). doi:10.1038/526631a

Authors: Nicole Dubilier, Margaret McFall-Ngai & Liping Zhao

Understanding how microbes affect health and the biosphere requires an international initiative, argue Nicole Dubilier, Margaret McFall-Ngai and Liping Zhao.

Institutions: Revive universities of the Muslim world

Nature 526, 7575 (2015). doi:10.1038/526634a

Authors: Nidhal Guessoum & Athar Osama

To boost science, higher-education institutes must give students a broad education and become meritocratic, say Nidhal Guessoum and Athar Osama.